NBDC Research ID: hum0533.v1
SUMMARY
Aims: In recent years, gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS), an autosomal dominant syndrome with polyp formation in the gastric cardia progressing to carcinoma, has been reported. Germline mutations in APC promoter 1B were identified as its cause, yet the molecular mechanisms of carcinogenesis remain unclear. To elucidate the progression from normal mucosa to fundic gland polyps (FGPs) and carcinoma, we collected multiple samples from each lesion and performed whole exome sequencing and RNA sequencing. Comprehensive mutational and transcriptomic analyses provided novel insights into GAPPS biology.
Methods: Whole exome sequencing, RNA sequencing
Participants/Materials: 7 GAPPS cases
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000843 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2025/10/17 |
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MOLECULAR DATA
| Participants/Materials |
GAPPS (ICD10: D139): 7 cases 61 samples (14 gastric carcinoma, 13 gastric polyp, 27 normal gastric mucosa, 7 peripheral blood) |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNA extracted from tumor tissues or non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V6 |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Software | GATK (v4.2.6.1), Picard MarkDuplicates (v2.27.5), Samtools (v1.14), ANNOVAR (2020-06-08 release) |
| Mapping Quality | Median MAPQ ≥ 60 |
| Reference Genome Sequence | GRCh38.p14 |
| Coverage (Depth) | 175x (range 144–236x) |
| QC Methods |
FastQC (v0.11.9) SNP: QD < 2.0, FS > 60.0, MQ < 40.0, MQRankSum < -12.5, ReadPosRankSum < -8.0, SOR > 3.0 INDEL: QD < 2.0, FS > 200.0, ReadPosRankSum < -20.0, SOR > 10.0 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000985 |
| Total Data Volume | 653.9 GB（bam, bai, csv） |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
GAPPS (ICD10: D139): 7 cases 53 samples (13 gastric carcinoma, 13 gastric polyp, 27 normal gastric mucosa) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNA extracted from tumor tissues or non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Ultra II RNA Library Prep Kit |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Softwear | STAR (v2.7.10a), RSEM (v1.3.3), Samtools (v1.14), DESeq2 (v1.38.3) |
| Mapping Quality | Median MAPQ ≥ 60 |
| Reference Genome Sequence | GRCh38.p14 |
| QC Methods |
FastQC (v0.11.9) SNP: QD < 2.0, FS > 60.0, MQ < 40.0, MQRankSum < -12.5, ReadPosRankSum < -8.0, SOR > 3.0 INDEL: QD < 2.0, FS > 200.0, ReadPosRankSum < -20.0, SOR > 10.0 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000985 |
| Total Data Volume | 653.9 GB（bam, bai, csv） |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Chihiro Matsumoto
Affiliation: Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Princess Takamatsu Cancer Research Fund | Molecular elucidation of the dysplasia–adenoma–adenocarcinoma sequence in gastric cancer | 21-25303 |
| Japanese Gastric Cancer Association | Comprehensive genomic analysis for molecular mechanism of carcinogenesis of hereditary gastric cancer | JGCA-32 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Elucidation of the carcinogenic mechanisms of hereditary gastric cancer and establishment of innovative therapeutic strategies | 24K10427 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Development of a precise method for estimating the timing of mutations during carcinogenesis | 24K18481 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genomic and transcriptomic landscape of carcinogenesis in patients with gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS) | ||
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
